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1.
The synthesis and some of the physical-chemical properties of tricopolymers of L -glutamic acid, L -lysine, and L -alanine are reported here. The molar ratios of the glutamyl: lysyl: alanyl residues were 1:1:X or 3:2:X, where the alanyl content X was increased in regular steps. The α-helix content calculated from the optical rotatory dispersion of the polypeptides is compared with a predicted helix content estimated from the composition of the polymers and the known behavior of the homopolypeptides at pH 3, 8, and 12. At pH 3 copolypeptides containing 20 mole-% or more alanine exhibit a helix content equal to the sum of their alanyl and glutamyl residue contents. At pH 8 the helix content equals the alanyl content when the latter was 40 mole-% or higher; at lower alanyl contents the electrostatic interaction between charged glutamyl and lysyl residues makes some contribution. At pH 12 the amount of helix observed is proportional to the mole ratio of alanine residues present in the polymer. The helix content of a tricopolymer containing 1:1:3 mole ratios of glutamyl: lysyl: alanyl residues was determined in solutions of lithium bromide and in urea solutions. Both reagents led to a decrease in helix content at pH 3 and 8 to a minimum of approximately 20% helix in 8M urea or 5.5M LiBr. The helix–random chain transition curves at pH 3 and 8 are parallel when the urea concentration is varied, but differ in shape when the lithium bromide concentration is varied at pH 3 and 8. The mode of action of these two “denaturing” reagents may thus be different. Heating the same tricopolypeptide at pH 3 or 8 from 5 to 80°C. also led to a helix–random chain transition centered at approximately 45°C.  相似文献   

2.
Dietmar Prschke 《Biopolymers》1971,10(10):1989-2013
The properties of oligonucleotide helices of adeuylic- and uridylic acid oligomers have been investigated by measurements of hypo-and hyperchromieity. High ionic strengths favor the formation of triple helices. Thus, the double helix-coil transition can be studied (without interference by triple helices) only at low ionic-strength. A “phase diagram” is given representing the Tm-values of the various transitions at different ionic strengths for the system A(pA)17 + U(pU)17. Oligonucleolides of chain lengths <8 always form both double and triple helices at the nucleotide concentrations required for base pairing. For this reason the double helix-coil transition without coupling of the triple helix equilibrium can only be measured for chain lengths higher than 7. Melting curves corresponding to this transition have been determined for chain lengths 8, 9, 10, 11, 14 and 18 at different concentrations. An increase in nucleotide concentration leads to an increase in melting temperature. The shorter the chain length the lower the Tm-value and the broader the helix-coil transition. The experimental transition curves have been analysed according to a staggering zipper model with consideration of the stacking of the adeuylic acid single strands and the electrostatic repulsion of tlip phosphate charges on opposite strands. The temperature dependence of the nucleation parameter has been accounted for by a slacking factor x. The stacking factor expresses the magnitude of the stacking enthalpy. By curve fitting xwas computed to be 0.7, corresponding to a stacking enthalpy of about S kcal/mole. The model described allows the reproduction of the experimental transition curves with relatively high accuracy. In an appendix the thermodynamic parameters of the stacking equilibrium of poly A and of the helix-coil equilibria of poly A + poly U at neutral pH are calculated (ΔHA = ?7.9 kcal/mole for the poly A stacking and ΔH12 = ?10.9 kcal/mole for the formation of the double helix from the randomly coiled single strands). A formula for the configurational entropy of polymers derived by Flory on the basis of a liquid lattice model is adapted to calculate the stacking entropies of adenylic oligomers.  相似文献   

3.
Y D Kim  I M Klotz 《Biopolymers》1972,11(2):431-441
The copolymer poly Glu42Lys28Ala30 was crosslinked by S–S bridges by reaction with butyrothiolactone followed by air oxidation of the mercaptan covalent adduct. The modified copolypeptide was more compact hydrodynamically, more resistant to the structurally disruptive effects of urea, and able to bind dye cations with much increased avidity.  相似文献   

4.
The consequences of incorporating non-complementary residues into the poly (I) · poly (C) helix have been investigated. Complexes of poly (I) and copolymers of C with different mole-ratios of I, A and U residues have been prepared and denatured in a variety of solvents. The results of both denaturation and analysis of the stoichiometry of the reactions suggest that in poly (I)· poly (C, Ix) complexes, the I residues are excluded from the helix matrix, whereas in the poly (I) · poly (C, Ux) and poly (I) · poly (C, Ax) systems the minor component bases are retained. Preliminaries to a quantitative analysis of the transition data are presented, permitting rough estimates of the difference in stability between poly (I) · poly (C) and poly (I) · poly (U) or poly (I) · poly (A) pairs in these complexes—the results being 1.7 kcal./mole and 1.3 kcal./mole, respectively. The differences in behavior of poly (I) · poly (C, I) complexes are found to be most evident in the presence of 8 m-urea.  相似文献   

5.
H Yamamoto  T Hayakawa  J T Yang 《Biopolymers》1974,13(6):1117-1125
Poly(Nδ-carbobenzoxy, Nδ-benzyl-L -ornithine) (PCBLO) was prepared by the standard NCA method. PCBLO was converted into poly(Nδ-benzyl-L -ornithine) (PBLO) through decarbobenzoxylation with hydrogen bromide. The monomer Nδ-benzyl-L -ornithine was synthesized by reacting L -ornithine with benzaldehyde, followed by hydrogenation. The conformation of the two polypeptides was studied by optical rotatory dispersion and circular dichroism. PCBLO forms a right-handed helix in helix-promoting solvents. In mixed solvents of chloroform and dichloroacetic acid (DCA) it undergoes a sharp helix–coil transition at 12% (v/v) DCA at 25°C, as compared with 36% for poly(Nδ-carbobenzoxy-L -ornithine) (PCLO). Like PCLO, the helix–coil transition is “inverse,” that is, high temperature favors the helical form. PBLO is soluble in water at pH below 7 and has a “coiled” conformation. In 88% (v/v) 1-propanol above pH (apparent) 9.6 it is completely helical. In 50% 1-propanol the transition pH (apparent) is about 7.4; this compares with a pHtr of about 10 for poly-L -ornithine in the same solvent.  相似文献   

6.
T E Gunter  K K Gunter 《Biopolymers》1972,11(3):667-678
Thermal denaturation of DNA's and the corresponding helix–coil transformation of artificial polyribonucleic and polydeoxyribonucleic acids have been studied extensively both theoretically1–13 and experimentally. 14–30 Much less work has been carried out on the properties of these polynucleic acids at high pressure, and in particular, on the presure dependence of the helix–coil transition temperature.31–33 Light-scattering techniques have been used in this study to measure the pressure dependence of the helix–coil transition temperature of the two- and three-stranded helices of polyriboadenylic and polyribouridilic acids and of calf thymus DNA. From the slopes of the transition temperature vs. pressure curves and heats of transition obtained from the literature,20,34 the following volume changes from these helix–coil transitions have been obtained: (a) ?0.96 cc/mole of nucleotide base pairs for the poly (A + U) transition, (b) +0.35 cc/mole of nucleotide base trios for the poly (A + 2U) transition, and (c) +2.7 cc/mole of nucleotide base pairs for the DNA transition. The relative magnitudes and signs of these volume changes which show that poly (A + U) is destabilized by increased pressure, whereas poly (A + 2U) and calf thymus DNA are stabilized by increased pressure, indicates that further development of the helix–coil transition theory for polynucleotides is needed.  相似文献   

7.
S Kubota  K Ikeda  J T Yang 《Biopolymers》1983,22(10):2219-2236
A series of sequential polypeptides, (Lysi-Alaj)n, and random copolypeptides, (Lysx, Alay)n, were synthesized. The competitive effect of Ala, a helix former, and Lys, whose homopolymer has a β-form in neutral NaDodSO4 solution, was determined by CD and absorption spectroscopy. All the polypeptides studied were unordered in neutral solution without the surfactant. Of the six sequential polypeptides only (Lys-Ala)n adopted a stable β-form in NaDodSO4 solution. Most striking is the difference between this polypeptide, (Lys2-Ala2)n and (Lysx, Alay)n, even though they all have equimolar Lys and Ala. (Lys2-Ala2)n was partially helical in 2.5–5 mM NaDodSO4 but approached the unordered form in 50 mM NaDodSO4, whereas (Lys50, Ala50)n was completely helical in all NaDodSO4 concentrations. Even Lysrich (Lys2-Ala)n and (Lys3-Ala)n formed a partial helix and a trace of the β-form, respectively, in low NaDodSO4 concentrations; both reverted to the unordered form in high NaDodSO4 concentrations. These results can be explained by Pauling-Corey's model for β-pleated sheets. Only (Lys-Ala)n has all DodSO-bound Lys+ residues on one side and Ala residues on the other side of the polypeptide chain. They can nestle quiet efficiently in a β-sheet and between neighboring β-sheets. Our results further imply that random copolypeptides are not completely random; they comprise varying segments of (Lysk-Alam), where k and m could vary from zero to a small integer.  相似文献   

8.
Base pairing equilibria between polynucleotides and complementary monomers   总被引:4,自引:0,他引:4  
R J Davies  N Davidson 《Biopolymers》1971,10(9):1455-1479
Equilibrium dialysis measurements and optical melting curve data have been used to study the formation and stability of a number of complexes between polynucleotides and complementary monomers. The cooperativity parameter, (dθ/d ln c)θ = 0.5, where θ is the fraction of U or C residues complexed, and c is the concentration of free monomer has been measured as 1.4 for the 2:1 poly U:d-adenosine-complex, and 2.05 for the 2:1 poly C:d-guanosiue complex at pH 7. The variation of Tm with c for several complexes has been used to calculate their partial molar enthalpies of formation at the midpoint of the transition: in 1.0 MNa + at pH 7, for the 2:1 complex of poly-U with 2-amino-adenine, this is ? 18.7 kcal/mole of 2-amino-adenine, for poly-U with adenosine it is ? 18.7 kcal/ mole; for poly-C with dG, it is ? 16.8 kcal/mole. These results do not agree very well with calorimetric integral heats of reaction reported in the literature.33 Complexes with random copolymers were also studied. The random copolymer, poly-UC, can form a mixed complex with dG and either dA or 2-amino-adenosine; the binding of dG is enhanced by an adenine derivative and vice versa.Similarly, poly AC can form a mixed complex with dG and 3-methyl-xanthine. In each case, it appears that the ideal composition is a 2:1 hydrogen-bonded complex, but the actual stoichiometry is such that each base on the random polynucleotide binds less than one-half of a molecule of its complementary monomer. Poly UG can bind dG and dA, but in a less cooperative and specific way.  相似文献   

9.
The NMR assignments of backbone 1H, 13C,and 15N resonances for calcium-bound human S100B werecompleted via heteronuclear multidimensional NMR spectroscopic techniques.NOE correlations, amide exchange, 3JHNHcoupling constants, and CSI analysis were used to identify the secondarystructure for Ca-S100B. The protein is comprised of four helices (helix I,Glu2-;Arg20; helix II,Glu31-;Asn38; helix III,Gln50-;Thr59; helix IV,Phe70-;Phe87), three loops (loop I,Glu21-;His25; loop II,Glu39-;Glu49; loop III,Leu60-;Gly66), and two -strands(strand I, Lys26>-;Lys28; strand II,Glu67-;Asp69) which form a shortantiparallel -sheet. Helix IV is extended by approximately one turnwhen compared to the secondary structures of apo-rat [Drohat et al. (1996)Biochemistry, 35, 11577-;11588] and bovine S100B [Kilby et al. (1996)Structure, 4, 1041-;1052]. In addition, several residues outside thecalcium-binding loops in S100B undergo significant backbone chemical shiftchanges upon binding calcium which are not observed in the related proteincalbindin D9k. Together these observations support previoussite-directed mutagenesis, absorption spectroscopy, and cysteine chemicalreactivity experiments, suggesting that the C-terminus in Ca-S100B isimportant for interactions with other proteins.  相似文献   

10.
Extensive conformational analysis of a series of β‐alkyl substituted cyclopeptides—cyclo(Pro1–Xaa2–Nle3–Ala4–Nle5–Pro6–Xaa7–Nle8–Ala9–Nle10) and cyclo[Pro1–Xaa2–Nle3–(Cys4– Nle5–Pro6–Xaa7–Nle8–Cys9)–Nle10] as well as their corresponding unsubstituted core structures cyclo(Pro1–Xaa2–Ala3–Ala4–Ala5–Pro6–Xaa7–Ala8–Ala9–Ala10) and cyclo(Pro1–Xaa2–Ala3–Cys4– Ala5–Pro6–Xaa7–Ala8–Cys9–Ala10) has been performed employing both the ECEPP/2 and the MAB force fields (Xaa = Gly, L ‐Ala, D ‐Ala, Aib, and D ‐Pro). Results show that (a) possible three‐dimensional structures of the cyclo(Pro1–Gly2–Lys3–Ala4–Lys5–Pro6–Gly7–Lys8–Ala9–Lys10) molecule are not limited to a single extended “rectangular” conformation with all Lys side chains oriented at the same side of the molecule; (b) conformational equilibrium in monocyclic analogues obtained by replacements of conformationally flexible Gly residues for L ‐Ala, D ‐Ala, Aib, or D ‐Pro is not significantly shifted towards the target “rectangular” conformational type; and (c) introduction of disulfide bridges between positions 4 and 9 is a very powerful way to stabilize the target conformations in the resulting bicyclic molecules. These findings form the basis for further design of rigidified regioselectively addressable functionalized templates with many application areas ranging from biostructural to diagnostic purposes. © 1999 John Wiley & Sons, Inc. Biopoly 50: 361–372, 1999  相似文献   

11.
The data presented in this paper characterize the immune responses in mice to the two related random terpolymers, poly(Glu57Lys38Tyr5) (GLT5) and poly (Glu55Lys34Tyr15) (GLT15), which are similar to the previously reported response against the terpolymer poly(Glu58Lys38Phe4) (GLØ). Responsiveness is linked to theH-2 d ,H-2 ja ,H-2 q andH-2 r haplotypes. The observed responsiveness of the recombinant strain B10.A(5R)tentatively maps theIr-GLT gene to the right of theIB subregion, i. e., in theIC subregion which codes for lymphocyte alloantigens. If confirmed this would be the firstIr gene to be mapped in theIC subregion.  相似文献   

12.
We have measured the thermodynamic parameters of the slow-fast tail-fiber reorientation transition on T2L bateriophage. Proportions of the virus in each form were determined from peak-height measurements in sedimention-velocity runs and from average diffusion coefficients obtained by quasielastic laser light scattering. Computer simulation of sedimentation confirmed that there were no undetected intermediates in the transition, which was analyzed as a two-state process. Van't Hoff-type plots of the apparent equilibrium constant and of the pH midpoint of the transition as function of reciprocal temperature led to the following estimates of the thermodynamic parameters for the transition at pH 6.0 and 20°C: ΔH° = ?139 ± 18Kcal mol?1, ΔS° = ?247 ± 46 cal K?1 mol?1, and ΔG° = ?66 ± 22 kcal mol?1. Per mole of protons taken up in the transition, the analogous quantities were ?15.9 ± 1.7 kcal mol?1, ?26.3 ± 2.2 cal K?1 mol?1, and ?8.22 ± 1.8 kcal mol?1. The net number of protons taken up was about 8.5 ± 1.5. The large values of the thermodynamic functions are consistent with a highly cooperative reaction and with multiple interactions between the fibres and the remainder of the phage. The negative entropy of the transition is probably due to immobilization of the fibres.  相似文献   

13.
Absorbance-temperature profiles have been determined for the following self-complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A2GCU2, A3GCU3, A4GCU4, A6CG + CGU6, A8CG + CGU8, A4G2 + C2U4, A5G2 + C2U5, A4G3 + C3U4, and A5G3 + C3U5. In all cases cooperative melting transitions indicate double-helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single-strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of ?15 kcal/mole. Due to the high degree of single-strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only ?5 to ?6 kcal/mole. (The corresponding parameters for AU pairs are ?10.7 kcal/mole and ?5 to ?6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in ΔH were seen among the sequence isomers. The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 105 to 107M?1 sec?1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence AnGCUn recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec?1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on AnGCUn helix formation showed that the rates of recombination increase considerably with increased ionic strength.  相似文献   

14.
According to the conserved sequences flanking the 3′ end of the 16S and the 5′ end of the 23S rDNAs, PCR primers were designed, and the 16S-23S rDNA intergenic spacers (IGSs) of two strains of Vibrio vulnificus were amplified by PCR and cloned into pGEM-T vector. Different clones were selected to be sequenced and the sequences were analyzed with BLAST and the software DNAstar. Analyses of the IGS sequences suggested that the strain ZSU006 contains five types of polymorphic 16S-23S rDNA intergenic spacers, namely, IGSGLAV, IGSGLV, IGSlA, IGSG and IGSA; while the strain CG021 has the same types of IGSs except lacking IGSA. Among these five IGS types, IGSGLAV is the biggest type, including the gene cluster of tRNAGlu - tRNALys - tRNAAla - tRNAVal; IGSGLV includes that of tRNAGlu-tRNALys-tRNAVal; IGSAG, tRNAAla-tRNAGlu; IGSIA, tRNAIle-tRNAAla; IGSG, tRNAGlu and IGSA, tRNAAla. Intraspecies multiple alignment of all the IGS sequences of these two strains with those of V. vulnificus ATCC27562 available at GenBank revealed several highly conserved sequence blocks in the non-coding regions flanking the tRNA genes within all of strains, most notably the first 40 and last 200 nucleotides, which can be targeted to design species-specific PCR primers or detection probes. The structural variations of the 16S-23S rDNA intergenic spacers lay a foundation for developing diagnostic methods for V. vulnificus.  相似文献   

15.
The thermal helix–coil transition of four samples of poly(γ-benzyl-L -glutamate) in the dioxane–dichloroacetic acid (DCA) mixture was studied by optical rotatory dispersion method. The transition occurred at very high DCA content (97.5% by weight) in this system. The transition parameters have been evaluated by two methods based on the theories of Zimm and Bragg and of Nagai. The values of the helix initiation parameter and of the enthalpy of transition were found to be (4.4 ± 0.4) × 10?5 and 340 cal/mole, respectively. The range of validity and equivalence of the two methods is discussed.  相似文献   

16.
In order to examine the helix-coil transition of water-insoluble polypeptides, without requiring interspersion of charged or polar residues within the sequence, a tri-block copolymer strategy has been developed to determine the helix propensity of amino acids in short (15-residue) peptides. The method is also well suited to evaluate specific interactions that contribute to helix formation. In this approach, measurement is made of the helix content of the central block of tri-block copolymers of the type Lys15-X-Lys15, where X is the 15-residue peptide whose helix content is being investigated. The suitability of tri-block copolymers of this type has been verified experimentally by using the water-soluble peptide (Ala2GlnAla2)3 as the central block. The CD spectrum of the central block in the tri-block copolymer and of Ac-(Ala2GlnAla2)3-NH2 are indistinguishable within experimental error. © 1996 John Wiley & Sons, Inc.  相似文献   

17.
Iwao Satake  Jen Tsi Yang 《Biopolymers》1975,14(9):1841-1846
The conformational phase diagram of poly(L -lysine) (4.6 × 10?4 M, residue) in sodium dodecyl sulfate (1.6 × 10?2 M) solution was constructed from circular dichroism results at various temperatures and pH's. Poly(L -lysine)–sodium dodecyl sulfate complexes undergo a β–helix transition upon raising the pH of the solution. The transition pH tends to shift downward at elevated temperatures. No helix–β transition can be detected for poly(L -lysine) in sodium dodecyl sulfate solution (pH > 11) even after 1-hr heating at 70°C. This is in marked contrast with uncharged poly(L -lysine) solution without sodium dodecyl sulfate, which is converted into the β-form upon mild heating of the solution above 50°C.  相似文献   

18.
Syntheses by conventional procedures of the three analogs corresponding to the porcine secretin sequence crossed at position 6 by the N-terminal hexapeptide sequences of VIP, GIP, and glucagon are described, viz., Ala4,Val5-, Tyr1,Ala2,Glu3-, and Gln3-secretin (VIP-SN, GIP-SN, and GLU-SN). The analog Phe1,Phe2,Trp3,Lys4-secretin (SOMA-SN), designed on the basis of the surprising homology of the sequence portions 10–13 of somatostatin and 5–8 of secretin, was also prepared. Finally, the synthesis of Nα-3-(4-hydroxyphenyl)propionyl-β-alanyl-secretin (DATA-SN), a tracer suitable for secretin radioimmunoassay and as an N-terminus modified secretin analog, is reported. The analogs are compared, in terms of their biological and immunological properties in different assay systems, with pure synthetic secretin.  相似文献   

19.
Histatin‐5 (Hst‐5, DSHAKRHHGYKRKFHEKHHSHRGY) is a member of a histidine‐rich peptide family secreted by major salivary glands, exhibiting high fungicidal activity against Candida albicans. In the present work, we demonstrate the 3D structure of the head‐to‐tail cyclic variant of Hst‐5 in TFE solution determined using NMR spectroscopy and molecular dynamics simulations. The cyclic histatin‐5 reveals a helix‐loop‐helix motif with α‐helices at positions Ala4‐His7 and Lys11‐Ser20. Both helical segments are arranged relative to each other at an angle of ca. 142°. The head‐to‐tail cyclization increases amphipathicity of the peptide, this, however, does not affect its antimicrobial potency. Copyright © 2014 European Peptide Society and John Wiley & Sons, Ltd.  相似文献   

20.
The course of the reversible helix formation of poly(γ-benzyl L -glutamate) (PBG) dissolved in a mixture of dichloroacetic acid (DCA) and 1,2-dichloroethane (EDC) was followed by measuring the heat capacity and the optical rotation of the system through the transition region. The results of these measurements indicate that the transition enthalpy ΔH the transition temperature Tc, and the Zimm-Bragg parameter σ depend considerably on the PBG concentration as well as on the composition of the solvent. For the standard state of infinite dilution, however, a linear extrapolation of the measured ΔH if values results in a standard value ΔH° = 950 cal./mole, independent of the solvent composition. The results of the calorimetric measurements are discussed in relationship to changes in optical rotation. Some peculiarities in the measured thermodynamic and optical properties in solutions with relatively high content of dichloroacetic acid are reported.  相似文献   

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